I encountered certain modded recipes in Space Exploration in which productivity will only affect some of the multiple products. The items not affected are being reported with lower than expected values, sometimes going into the negative.

Example: (assuming crafting speed of 1)
Crushed Holminite - inputs 2 ore, outputs 1 crushed ore, 25% stone
with 8% productivity - stone output is 0.19/s
with 32% productivity - stone output is 0.01/s

I'm experiencing the same issue.
Playing Space Exploration, the rates for any machine crafting a recipe with byproducts and using productivity modules is incorrect.
My understanding is that when crafting a recipe with byproducts and using productivity modules, only the actual product receives productivity bonuses, and the byproducts don't.
Using this rate calculator correctly calculates the actual product, but incorrectly calculates any byproducts.

I'd love a fix to this problem, but looks like the mod creator is inactive at this point, so I'm not too hopeful for a fix.